This may not be exactly the sort of reply you're seeking, but hopefully it'll help some.
Firstly, the level draining effect from Ennervation is quite temporary...I see no reason that death would change that. After a few hours pass, the excess "negative energy" passes from the corpse just as it would from a living body. So there's that.
More to the point though, and I fully agree that this is not really made clear in the rules, I've always been of the opinion that when you die things kind of "reset," physically, at least. Which is to say that negative levels and magic stat draining effects cease to operate. Those things typically target only the living, after all. Once a being is no longer living, he's also no longer a valid target for that effect. Thus, the effect ceases to operate. Granted, that cessation in no way alters the dead status it brought about.
For example, a wraith ecto-claws our buddy Bob. Bob is lamentably first level. It drains him down to 1 Con before we can zorch it...but unfortunately a goblin with a crossbow finishes him off in his weakened state. Note that Bob died this way because otherwise he'd become a wraith, which complicates things a bit.
Can Bob be raised?
The rules are not clear, but I believe the answer is (should be) yes.
A corpse has no Con score. When Bob became a corpse, he lost his Con score. No Con score means he can't be affected by Con drain. Raising him restores his Con score...not to the temporarily reduced value (because that effect ended when he lost his Con score), but to its original value. Then he loses a point, but is very much alive.
Similarly, Wizzy the Amazing Archmage does his horrid TimeStop + 4 Maximized Energy Drains, inflicting a whopping 32 negative levels on his rival...Tim. Tim is very powerful...but he's not level 33. Thus, Tim is dead.
Normally those negative levels would persist for 24 hours, allow Fort saves, and THEN become permanant...but in this case that's moot. He's dead, and he ain't comin' back. But can Tim be raised?
Again, I think the answer is yes.
Dead things don't have levels. When Tim becomes a corpse, he becomes an invalid target for negative levels. Thus, the negative levels are no longer affecting him. They don't magically reappear when Tim is resurrected. Not unless Wizzy shows up again and starts blastin'.
This is the way I'd do it mainly because it seems fair, it avoids a lot of thorny problems (that you yourself have pointed out) and it's at least nominally defensible using existing rules. I'd be the first to admit it's pretty much an individual interpretation...there is no explicit coverage of that particular issue that I'm aware of in the books. But it's a reasonable inference, I think, and it's fair in that it doesn't penalize characters who die by some means and not others.
Of course, a smart caster always has a Clone handy anyway. That neatly sidesteps all woes.
